**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=5vpe.pdb -o=5vpe.out File name: 5vpe.pdb no. of DNA/RNA chains: 4 [E=18,F=18,G=18,H=18] no. of nucleotides: 72 no. of atoms: 7094 no. of waters: 228 no. of metals: 3 [Na=3] **************************************************************************** List of 36 base pairs nt1 nt2 bp name Saenger LW DSSR 1 G.DG2 H.DC18 G-C WC 19-XIX cWW cW-W 2 G.DT3 H.DA17 T-A WC 20-XX cWW cW-W 3 G.DC4 H.DG16 C-G WC 19-XIX cWW cW-W 4 G.DG5 H.DC15 G-C WC 19-XIX cWW cW-W 5 G.DG6 H.DC14 G-C WC 19-XIX cWW cW-W 6 G.DT7 H.DA13 T-A WC 20-XX cWW cW-W 7 G.DG8 H.DC12 G-C WC 19-XIX cWW cW-W 8 G.DA9 H.DT11 A-T WC 20-XX cWW cW-W 9 G.DC10 H.DG10 C-G WC 19-XIX cWW cW-W 10 G.DT11 H.DA9 T-A WC 20-XX cWW cW-W 11 G.DC12 H.DG8 C-G WC 19-XIX cWW cW-W 12 G.DA13 H.DT7 A-T WC 20-XX cWW cW-W 13 G.DC14 H.DG6 C-G WC 19-XIX cWW cW-W 14 G.DC15 H.DG5 C-G WC 19-XIX cWW cW-W 15 G.DG16 H.DC4 G-C WC 19-XIX cWW cW-W 16 G.DA17 H.DT3 A-T WC 20-XX cWW cW-W 17 G.DC18 H.DG2 C-G WC 19-XIX cWW cW-W 18 G.DG19 H.DC1 G-C WC 19-XIX cWW cW-W 19 E.DG2 F.DC18 G-C WC 19-XIX cWW cW-W 20 E.DT3 F.DA17 T-A WC 20-XX cWW cW-W 21 E.DC4 F.DG16 C-G WC 19-XIX cWW cW-W 22 E.DG5 F.DC15 G-C WC 19-XIX cWW cW-W 23 E.DG6 F.DC14 G-C WC 19-XIX cWW cW-W 24 E.DT7 F.DA13 T-A WC 20-XX cWW cW-W 25 E.DG8 F.DC12 G-C WC 19-XIX cWW cW-W 26 E.DA9 F.DT11 A-T WC 20-XX cWW cW-W 27 E.DC10 F.DG10 C-G WC 19-XIX cWW cW-W 28 E.DT11 F.DA9 T-A WC 20-XX cWW cW-W 29 E.DC12 F.DG8 C-G WC 19-XIX cWW cW-W 30 E.DA13 F.DT7 A-T WC 20-XX cWW cW-W 31 E.DC14 F.DG6 C-G WC 19-XIX cWW cW-W 32 E.DC15 F.DG5 C-G WC 19-XIX cWW cW-W 33 E.DG16 F.DC4 G-C WC 19-XIX cWW cW-W 34 E.DA17 F.DT3 A-T WC 20-XX cWW cW-W 35 E.DC18 F.DG2 C-G WC 19-XIX cWW cW-W 36 E.DG19 F.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 helices Note: a helix is defined by base-stacking interactions, regardless of bp type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[1] bps=18 strand-1 5'-GTCGGTGACTCACCGACG-3' bp-type |||||||||||||||||| strand-2 3'-CAGCCACTGAGTGGCTGC-5' helix-form BBBBBBBBBBBBBBBBB 1 G.DG2 H.DC18 G-C WC 19-XIX cWW cW-W 2 G.DT3 H.DA17 T-A WC 20-XX cWW cW-W 3 G.DC4 H.DG16 C-G WC 19-XIX cWW cW-W 4 G.DG5 H.DC15 G-C WC 19-XIX cWW cW-W 5 G.DG6 H.DC14 G-C WC 19-XIX cWW cW-W 6 G.DT7 H.DA13 T-A WC 20-XX cWW cW-W 7 G.DG8 H.DC12 G-C WC 19-XIX cWW cW-W 8 G.DA9 H.DT11 A-T WC 20-XX cWW cW-W 9 G.DC10 H.DG10 C-G WC 19-XIX cWW cW-W 10 G.DT11 H.DA9 T-A WC 20-XX cWW cW-W 11 G.DC12 H.DG8 C-G WC 19-XIX cWW cW-W 12 G.DA13 H.DT7 A-T WC 20-XX cWW cW-W 13 G.DC14 H.DG6 C-G WC 19-XIX cWW cW-W 14 G.DC15 H.DG5 C-G WC 19-XIX cWW cW-W 15 G.DG16 H.DC4 G-C WC 19-XIX cWW cW-W 16 G.DA17 H.DT3 A-T WC 20-XX cWW cW-W 17 G.DC18 H.DG2 C-G WC 19-XIX cWW cW-W 18 G.DG19 H.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=18 strand-1 5'-GTCGGTGACTCACCGACG-3' bp-type |||||||||||||||||| strand-2 3'-CAGCCACTGAGTGGCTGC-5' helix-form BBBBBBBBBBBBBBBBB 1 E.DG2 F.DC18 G-C WC 19-XIX cWW cW-W 2 E.DT3 F.DA17 T-A WC 20-XX cWW cW-W 3 E.DC4 F.DG16 C-G WC 19-XIX cWW cW-W 4 E.DG5 F.DC15 G-C WC 19-XIX cWW cW-W 5 E.DG6 F.DC14 G-C WC 19-XIX cWW cW-W 6 E.DT7 F.DA13 T-A WC 20-XX cWW cW-W 7 E.DG8 F.DC12 G-C WC 19-XIX cWW cW-W 8 E.DA9 F.DT11 A-T WC 20-XX cWW cW-W 9 E.DC10 F.DG10 C-G WC 19-XIX cWW cW-W 10 E.DT11 F.DA9 T-A WC 20-XX cWW cW-W 11 E.DC12 F.DG8 C-G WC 19-XIX cWW cW-W 12 E.DA13 F.DT7 A-T WC 20-XX cWW cW-W 13 E.DC14 F.DG6 C-G WC 19-XIX cWW cW-W 14 E.DC15 F.DG5 C-G WC 19-XIX cWW cW-W 15 E.DG16 F.DC4 G-C WC 19-XIX cWW cW-W 16 E.DA17 F.DT3 A-T WC 20-XX cWW cW-W 17 E.DC18 F.DG2 C-G WC 19-XIX cWW cW-W 18 E.DG19 F.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems Note: a stem is defined as a helix consisting of only canonical WC/wobble pairs, with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=18 strand-1 5'-GTCGGTGACTCACCGACG-3' bp-type |||||||||||||||||| strand-2 3'-CAGCCACTGAGTGGCTGC-5' helix-form BBBBBBBBBBBBBBBBB 1 G.DG2 H.DC18 G-C WC 19-XIX cWW cW-W 2 G.DT3 H.DA17 T-A WC 20-XX cWW cW-W 3 G.DC4 H.DG16 C-G WC 19-XIX cWW cW-W 4 G.DG5 H.DC15 G-C WC 19-XIX cWW cW-W 5 G.DG6 H.DC14 G-C WC 19-XIX cWW cW-W 6 G.DT7 H.DA13 T-A WC 20-XX cWW cW-W 7 G.DG8 H.DC12 G-C WC 19-XIX cWW cW-W 8 G.DA9 H.DT11 A-T WC 20-XX cWW cW-W 9 G.DC10 H.DG10 C-G WC 19-XIX cWW cW-W 10 G.DT11 H.DA9 T-A WC 20-XX cWW cW-W 11 G.DC12 H.DG8 C-G WC 19-XIX cWW cW-W 12 G.DA13 H.DT7 A-T WC 20-XX cWW cW-W 13 G.DC14 H.DG6 C-G WC 19-XIX cWW cW-W 14 G.DC15 H.DG5 C-G WC 19-XIX cWW cW-W 15 G.DG16 H.DC4 G-C WC 19-XIX cWW cW-W 16 G.DA17 H.DT3 A-T WC 20-XX cWW cW-W 17 G.DC18 H.DG2 C-G WC 19-XIX cWW cW-W 18 G.DG19 H.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=18 strand-1 5'-GTCGGTGACTCACCGACG-3' bp-type |||||||||||||||||| strand-2 3'-CAGCCACTGAGTGGCTGC-5' helix-form BBBBBBBBBBBBBBBBB 1 E.DG2 F.DC18 G-C WC 19-XIX cWW cW-W 2 E.DT3 F.DA17 T-A WC 20-XX cWW cW-W 3 E.DC4 F.DG16 C-G WC 19-XIX cWW cW-W 4 E.DG5 F.DC15 G-C WC 19-XIX cWW cW-W 5 E.DG6 F.DC14 G-C WC 19-XIX cWW cW-W 6 E.DT7 F.DA13 T-A WC 20-XX cWW cW-W 7 E.DG8 F.DC12 G-C WC 19-XIX cWW cW-W 8 E.DA9 F.DT11 A-T WC 20-XX cWW cW-W 9 E.DC10 F.DG10 C-G WC 19-XIX cWW cW-W 10 E.DT11 F.DA9 T-A WC 20-XX cWW cW-W 11 E.DC12 F.DG8 C-G WC 19-XIX cWW cW-W 12 E.DA13 F.DT7 A-T WC 20-XX cWW cW-W 13 E.DC14 F.DG6 C-G WC 19-XIX cWW cW-W 14 E.DC15 F.DG5 C-G WC 19-XIX cWW cW-W 15 E.DG16 F.DC4 G-C WC 19-XIX cWW cW-W 16 E.DA17 F.DT3 A-T WC 20-XX cWW cW-W 17 E.DC18 F.DG2 C-G WC 19-XIX cWW cW-W 18 E.DG19 F.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5vpe nts=72 [whole] GTCGGTGACTCACCGACG&CGTCGGTGAGTCACCGAC>CGGTGACTCACCGACG&CGTCGGTGAGTCACCGAC ((((((((((((((((((&))))))))))))))))))&((((((((((((((((((&)))))))))))))))))) >5vpe-G #1 nts=18 3.29(0.31) [chain] DNA GTCGGTGACTCACCGACG (((((((((((((((((( >5vpe-H #2 nts=18 3.30(0.35) [chain] DNA CGTCGGTGAGTCACCGAC )))))))))))))))))) >5vpe-E #3 nts=18 3.24(0.30) [chain] DNA GTCGGTGACTCACCGACG (((((((((((((((((( >5vpe-F #4 nts=18 3.28(0.33) [chain] DNA CGTCGGTGAGTCACCGAC )))))))))))))))))) **************************************************************************** Summary of structural features of 72 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 G ( G.DG2 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 2 T ( G.DT3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 C ( G.DC4 0.004 anti,BI,canonical,non-pair-contact,helix,stem 4 G ( G.DG5 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 G ( G.DG6 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 T ( G.DT7 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 7 G ( G.DG8 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 A ( G.DA9 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 C ( G.DC10 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 T ( G.DT11 0.005 anti,BI,canonical,non-pair-contact,helix,stem 11 C ( G.DC12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 A ( G.DA13 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ( G.DC14 0.006 anti,BI,canonical,non-pair-contact,helix,stem 14 C ( G.DC15 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ( G.DG16 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 A ( G.DA17 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ( G.DC18 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 18 G ( G.DG19 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 19 C ) H.DC1 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 20 G ) H.DG2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 T ) H.DT3 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 C ) H.DC4 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 23 G ) H.DG5 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 G ) H.DG6 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 T ) H.DT7 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 G ) H.DG8 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 27 A ) H.DA9 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 28 G ) H.DG10 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 T ) H.DT11 0.006 anti,BI,canonical,non-pair-contact,helix,stem 30 C ) H.DC12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 A ) H.DA13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 32 C ) H.DC14 0.003 anti,BI,canonical,non-pair-contact,helix,stem 33 C ) H.DC15 0.003 anti,BI,canonical,non-pair-contact,helix,stem 34 G ) H.DG16 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 35 A ) H.DA17 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 36 C ) H.DC18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 37 G ( E.DG2 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 38 T ( E.DT3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 39 C ( E.DC4 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 40 G ( E.DG5 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 41 G ( E.DG6 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 42 T ( E.DT7 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 43 G ( E.DG8 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 44 A ( E.DA9 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 45 C ( E.DC10 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 46 T ( E.DT11 0.005 anti,BI,canonical,non-pair-contact,helix,stem 47 C ( E.DC12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 48 A ( E.DA13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 49 C ( E.DC14 0.005 anti,BI,canonical,non-pair-contact,helix,stem 50 C ( E.DC15 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 51 G ( E.DG16 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 52 A ( E.DA17 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 53 C ( E.DC18 0.006 anti,BI,canonical,non-pair-contact,helix,stem 54 G ( E.DG19 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 55 C ) F.DC1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 56 G ) F.DG2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 57 T ) F.DT3 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 58 C ) F.DC4 0.005 anti,BI,canonical,non-pair-contact,helix,stem 59 G ) F.DG5 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 60 G ) F.DG6 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 61 T ) F.DT7 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 62 G ) F.DG8 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 63 A ) F.DA9 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 64 G ) F.DG10 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 65 T ) F.DT11 0.008 anti,BI,canonical,non-pair-contact,helix,stem 66 C ) F.DC12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 67 A ) F.DA13 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 68 C ) F.DC14 0.004 anti,BI,canonical,non-pair-contact,helix,stem 69 C ) F.DC15 0.002 anti,BI,canonical,non-pair-contact,helix,stem 70 G ) F.DG16 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 71 A ) F.DA17 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 72 C ) F.DC18 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 7 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names